UC San Diego
COGS 137 - Fall 2024
2024-10-04
Q: Does R let you perform arithmetic across number and integer types?
A: Yup! For example7L + 2gives you 9. (Similarly7L + 2.2gives 9.2)
Q: I am confused on how to open up projects, what it means to comit and pull.
A: We’ll review this again today!
Q: I am very new to using Github, so using Github is a bit confusing, but probably just b/c I am very new to it.
A: This is a normal feeling at the start of this course! I promise in a week it will feel more comfortable!
Q: I’m curious about the usage of R versus Python. Are there certain situations where R is more useful than Python?
A: In a nutshell, almost everything you can do in one you can do in the other. However, in my opinion, R is most useful when 1) cleaning data, 2) using statistical models, and 3) visualizing data. (On the flip side, when I’m writing software, using APIs, and gathering data, I typically turn to Python.)
Q: How do I save my lecture practice into a new file in R?
A: I would recommend opening a new .Rmd file and then saving it with the name of the lecture.
Q: i noticed that global variables remain in the environment panel even when i delete that variable in my rmd script. does it matter that they are still there? i tried clicking the broom and rerunning the code, and only the variables i wanted remained, but is this the right way to go about changing or deleting variables in my code?
A: Yup! The broom will clean up your environment! There is also anrm()function if you ever want to remove an individual variable from your environment.
Q: Am I supposed to create an “R Markdown” or an “R Notebook”?
A: I’ll demo R Markdown, so encouraging use of that.
Q: Will we be covering any syntax guidelines when programming in R? For example, in other programming languages indents/spaces are necessary for many functions but I’m wondering if there is anything like that used in R.
A: I will highlight them as we go! R does not necessitate whitespace ever, but stylistically, we will encourage it. What I teach will be based off of this style guide.
Q: How many points are there in total for the extra credits
A: I’m not totally sure yet. At least a few points.
Q: I wonder what will be the format of the lab session?
A: Typically a short presentation (5 min) at the beginning to explain the lab or discuss the most difficult/confusing part. Then, time to work on lab and get questions answered by staff.
Q: Could you please post the slides one or two days before class? I would like to review them in advance so I can better follow along during the lecture and not feel lost. A: I totally understand the request, and I’ll do my best! (For example, these have been up since Monday), but I’m re-doing the slides up to class many days. While the examples will change this quarter, the concepts will overlap with last Fall, so feel free to reference those notes.
Q: What are the main parts of the R interface that we will be interacting with?
A: RMarkdown files, R Console, Git pane, Files pane, and Plots pane
Q: I had a question about the survey for participation. I’m usually busy right after class. Is there any way to get credit for it even if I submit it a couple of hours later or for it to open a little before class ends.
A: I do typically end class a few minutes early for completion then and we’re working to open it a few minutes before class ends. It’s always fine to fill it out later if it’s open. It will always be open until at least 5PM.
Due Dates:
Note:
options(download.file.method="wget")Source: https://academic.oup.com/clinchem/article/59/3/478/5621997
Evidence suggests recent smoking and/or blood THC concentrations 2–5 ng/mL are associated with substantial driving impairment, particularly in occasional smokers.link
As of 2021…link
Various approaches:
Focus here: Can we identify a biomarker of recent use?
Which compound, in which matrix, and at what cutoff is the best biomarker of recent use?
Source: Hoffman et al.
Participants were:
Source: Fitzgerald et al.
Source: Hoffman et al.
Source: Hoffman et al.
Source: Hoffman et al.
Three matrices:
Variables:
ID | participants identifierTreatment | placebo, 5.90%, 13.40%Group | Occasional user, Frequent userTimepoint | indicator of which point in the timeline participant’s collection occurredtime.from.start | number of minutes from consumptionYou’ll have access once your groups/repos are created…(today I want people to follow along; there will be time to try on your own soon!)
Where We’re Headed…
Results from: Hubbard et al (2021) Biomarkers of Recent Cannabis Use in Blood, Oral Fluid and Breath link
…and if there’s time PPV and Accuracy post 3h
Source: Fiztgerald et al.